@string{DRBentley = "Bentley, D. R."}
@string{HJCBerendsen = "Berendsen, Herman J. C."}
@string{KBergSorensen = "Berg-S\orensen, K"}
+@string{EBergantino = "Bergantino, Elisabetta"}
@string{DBerk = "Berk, D."}
@string{FBerkemeier = "Berkemeier, Felix"}
@string{BBerne = "Berne, Bruce J."}
@string{TBruls = "Bruls, T."}
@string{VBrumfeld = "Brumfeld, Vlad"}
@string{JDBryngelson = "Bryngelson, J. D."}
+@string{LBubacco = "Bubacco, Luigi"}
@string{JBuckheit = "Buckheit, Jonathan B."}
@string{ABuguin = "Buguin, A."}
@string{ABulhassan = "Bulhassan, Ahmed"}
@string{JClarkson = "Clarkson, John"}
@string{HClausen-Schaumann = "Clausen-Schaumann, H."}
@string{JMClaverie = "Claverie, J. M."}
+@string{WWCleland = "Cleland, W.~W."}
@string{KClerc-Blankenburg = "Clerc-Blankenburg, K."}
@string{NJCobb = "Cobb, Nathan J."}
@string{GHCohen = "Cohen, G.~H."}
@string{JCompP = "Journal of Computational Physics"}
@string{JEChem = "Journal of Electroanalytical Chemistry"}
@string{JMathBiol = "J Math Biol"}
-@string{JMicro = "Journal of microscopy"}
-@string{JPhysio = "Journal of physiology"}
-@string{JStructBiol = "Journal of structural biology"}
+@string{JMicro = "Journal of Microscopy"}
+@string{JPhysio = "Journal of Physiology"}
+@string{JStructBiol = "Journal of Structural Biology"}
@string{JTB = "J Theor Biol"}
@string{JMB = "Journal of Molecular Biology"}
@string{JP:CM = "Journal of Physics: Condensed Matter"}
@string{WMajoros = "Majoros, W."}
@string{DEMakarov = "Makarov, Dmitrii E."}
@string{RMamdani = "Mamdani, Reneeta"}
+@string{SMammi = "Mammi, Stefano"}
@string{EMandello = "Mandello, Enrico"}
@string{GManderson = "Manderson, Gavin"}
@string{FMann = "Mann, F."}
@string{BMurphy = "Murphy, B."}
@string{SMurphy = "Murphy, S."}
@string{AMuruganujan = "Muruganujan, A."}
+@string{FMusiani = "Musiani, Francesco"}
@string{EWMyers = "Myers, E. W."}
@string{RMMyers = "Myers, R. M."}
@string{AMylonakis = "Mylonakis, Andreas"}
@string{PA = "Pfl{\"u}gers Archiv: European journal of physiology"}
@string{PTRSL = "Philosophical Transactions of the Royal Society of London"}
@string{PR:E = "Phys Rev E Stat Nonlin Soft Matter Phys"}
-@string{PRL = "Physical review letters"}
+@string{PRL = "Physical Review Letters"}
%string{PRL = "Phys Rev Lett"}
@string{Physica = "Physica"}
@string{GPing = "Ping, Guanghui"}
@string{MPlumbley = "Plumbley, Mark"}
@string{PLOS:ONE = "PLOS ONE"}
%string{PLOS:ONE = "Public Library of Science ONE"}
+@string{PLOS:BIO = "PLOS Biology"}
@string{DPlunkett = "Plunkett, David"}
@string{PPodsiadlo = "Podsiadlo, Paul"}
@string{ASPolitou = "Politou, A. S."}
@string{THEMath = "Technische Hogeschool Eindhoven, Nederland,
Onderafdeling der Wiskunde"}
@string{SJBTendler = "Tendler, S.~J.~B."}
+@string{ITessari = "Tessari, Isabella"}
@string{STeukolsky = "Teukolsky, S."}
@string{CJ = "The Computer Journal"}
@string{JBC = "The Journal of Biological Chemistry"}
@string{UIP:Urbana = "University of Illinois Press, Urbana"}
@string{UTMB = "University of Texas Medical Branch"}
@string{MUrbakh = "Urbakh, M."}
+@string{FValle = "Valle, Francesco"}
@string{KJVanVliet = "Van Vliet, Krystyn J."}
@string{PVandewalle = "Vandewalle, Patrick"}
@string{CVech = "Vech, C."}
@book{ NIST:ESH,
editor = CCroarkin #" and "# PTobias,
author = NIST:SEMATECH,
- title = {e-Handbook of Statistical Methods},
+ title = {e-{H}andbook of Statistical Methods},
year = 2013,
month = may,
publisher = NIST:SEMATECH,
@article { bedard08,
author = SBedard #" and "# MMGKrishna #" and "# LMayne #" and "#
SWEnglander,
- title = "Protein folding: independent unrelated pathways or predetermined
+ title = "Protein folding: Independent unrelated pathways or predetermined
pathway with optional errors.",
year = 2008,
month = may,
project = "Cantilever Calibration"
}
+@article{ jaschke95,
+ author = MJaschke #" and "# HJButt,
+ title = {Height calibration of optical lever atomic force
+ microscopes by simple laser interferometry},
+ journal = RSI,
+ year = 1995,
+ volume = 66,
+ number = 2,
+ pages = {1258--1259},
+ publisher = AIP,
+ url = {http://rsi.aip.org/resource/1/rsinak/v66/i2/p1258_s1},
+ doi = {10.1063/1.1146018},
+ issn = {0034-6748},
+ keywords = {atomic force microscopy;calibration;interferometry;laser
+ beam applications;mirrors;spatial resolution},
+ abstract = {A new and simple interferometric method for height
+ calibration of AFM piezo scanners is presented. Except for a small
+ mirror no additional equipment is required since the fixed
+ wavelength of the laser diode is used as a calibration
+ standard. The calibration is appliable in the range between
+ several ten nm and several μm. Besides vertical calibration many
+ problems of piezo elements like hysteresis, nonlinearity, creep,
+ derating, etc. and their dependence on scan parameters or
+ temperature can be investigated.},
+}
+
@article { cao07,
author = YCao #" and "# MBalamurali #" and "# DSharma #" and "# HLi,
title = "A functional single-molecule binding assay via force spectroscopy",
@article { collins03,
author = FSCollins #" and "# MMorgan #" and "# APatrinos,
- title = "The Human Genome Project: lessons from large-scale biology.",
+ title = "The Human Genome Project: Lessons from large-scale biology.",
year = 2003,
month = apr,
day = 11,
the barrel. Quantitative analysis of force distributions and
lifetimes lead to a detailed picture of the complex mechanical
unfolding pathway through a rough energy landscape.",
- note = "Nice energy-landscape-to-one-dimension compression graphic.
- Unfolding Green Flourescent Protein (GFP) towards using it as an
- embedded force probe.",
+ note = "Towards use of Green Flourescent Protein (GFP) as an
+ embedded force probe. Nice energy-landscape-to-one-dimension
+ compression graphic.",
project = "Energy landscape roughness"
}
author = OKDudko #" and "# JMathe #" and "# ASzabo #" and "# AMeller #" and
"# GHummer,
title = "Extracting kinetics from single-molecule force spectroscopy:
- nanopore unzipping of {DNA} hairpins",
+ Nanopore unzipping of {DNA} hairpins",
year = 2007,
month = jun,
day = 15,
force techniques.",
note = "Develops Kramers improvement on Bell model for domain unfolding.
Presents unfolding under variable loading rates. Often cited as the
- ``Bell-Evans'' model? They derive a unitless treatment, scaling force
+ ``Bell--Evans'' model. They derive a unitless treatment, scaling force
by $f_\beta$, TODO; time by $\tau_f$, TODO; elasiticity by compliance
$c(f)$. The appendix has relaxation time formulas for WLC and FJC
polymer models.",
@article { hanggi90,
author = PHanggi #" and "# PTalkner #" and "# MBorkovec,
- title = "Reaction-rate theory: fifty years after {K}ramers",
+ title = "Reaction-rate theory: Fifty years after {K}ramers",
year = 1990,
month = "Apr",
journal = RMP,
@article { hutter05,
author = JHutter,
- title = "Comment on tilt of atomic force microscope cantilevers: effect on
+ title = "Comment on tilt of atomic force microscope cantilevers: Effect on
spring constant and adhesion measurements.",
year = 2005,
month = mar,
@article { improta96,
author = SImprota #" and "# ASPolitou #" and "# APastore,
- title = "Immunoglobulin-like modules from titin {I}-band: extensible
+ title = "Immunoglobulin-like modules from titin {I}-band: Extensible
components of muscle elasticity.",
year = 1996,
month = mar,
@article { klimov99,
author = DKlimov #" and "# DThirumalai,
- title = "Stretching single-domain proteins: phase diagram and kinetics of
+ title = "Stretching single-domain proteins: Phase diagram and kinetics of
force-induced unfolding",
year = 1999,
month = may,
@article{ labeit95,
author = SLabeit #" and "# BKolmerer,
- title = "Titins: giant proteins in charge of muscle ultrastructure
+ title = "Titins: Giant proteins in charge of muscle ultrastructure
and elasticity.",
journal = SCI,
year = 1995,
@article { levy02,
author = RLevy #" and "# MMaaloum,
title = "Measuring the spring constant of atomic force microscope
- cantilevers: thermal fluctuations and other methods",
+ cantilevers: Thermal fluctuations and other methods",
year = 2002,
journal = NT,
volume = 13,
@article { metropolis87,
author = NMetropolis,
- title = "The Beginning of the Monte Carlo Method",
+ title = "The Beginning of the {M}onte {C}arlo Method",
year = 1987,
journal = LAS,
volume = 15,
year = 1965,
publisher = McGraw-Hill,
address = "New York",
- note = "Thermal noise for SHOs, in Chapter 15, Sections 6 and 10.",
+ note = "Thermal noise for simple harmonic oscillators, in Chapter
+ 15, Sections 6 and 10.",
project = "Cantilever Calibration"
}
@article { walton08,
author = EBWalton #" and "# SLee #" and "# KJVanVliet,
- title = "Extending {B}ell's model: how force transducer stiffness alters
+ title = "Extending {B}ell's model: How force transducer stiffness alters
measured unbinding forces and kinetics of molecular complexes",
year = 2008,
month = apr,
pulling speed.},
}
+@article{ sandal08,
+ author = MSandal #" and "# FValle #" and "# ITessari #" and "#
+ SMammi #" and "# EBergantino #" and "# FMusiani #" and "#
+ MBrucale #" and "# LBubacco #" and "# BSamori,
+ title = {Conformational Equilibria in Monomeric $\alpha$-Synuclein
+ at the Single-Molecule Level},
+ year = 2008,
+ month = jan,
+ address = {Department of Biochemistry G. Moruzzi,
+ University of Bologna, Bologna, Italy.},
+ journal = PLOS:BIO,
+ volume = 6,
+ number = 1,
+ pages = {e6},
+ issn = {1545-7885},
+ doi = {10.1371/journal.pbio.0060006},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/18198943},
+ language = {eng},
+ keywords = {Buffers},
+ keywords = {Circular Dichroism},
+ keywords = {Copper},
+ keywords = {Entropy},
+ keywords = {Models, Molecular},
+ keywords = {Molecular Sequence Data},
+ keywords = {Mutation},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Protein Structure, Tertiary},
+ keywords = {alpha-Synuclein},
+ abstract = {Human $\alpha$-Synuclein ($\alpha$Syn) is a natively
+ unfolded protein whose aggregation into amyloid fibrils is
+ involved in the pathology of Parkinson disease. A full
+ comprehension of the structure and dynamics of early intermediates
+ leading to the aggregated states is an unsolved problem of
+ essential importance to researchers attempting to decipher the
+ molecular mechanisms of $\alpha$Syn aggregation and formation of
+ fibrils. Traditional bulk techniques used so far to solve this
+ problem point to a direct correlation between $\alpha$Syn's unique
+ conformational properties and its propensity to aggregate, but
+ these techniques can only provide ensemble-averaged information
+ for monomers and oligomers alike. They therefore cannot
+ characterize the full complexity of the conformational equilibria
+ that trigger the aggregation process. We applied atomic force
+ microscopy-based single-molecule mechanical unfolding methodology
+ to study the conformational equilibrium of human wild-type and
+ mutant $\alpha$Syn. The conformational heterogeneity of monomeric
+ $\alpha$Syn was characterized at the single-molecule level. Three
+ main classes of conformations, including disordered and
+ ``$\beta$-like'' structures, were directly observed and quantified
+ without any interference from oligomeric soluble forms. The
+ relative abundance of the ``$\beta$-like'' structures
+ significantly increased in different conditions promoting the
+ aggregation of $\alpha$Syn: the presence of \Cu, the pathogenic
+ A30P mutation, and high ionic strength. This methodology can
+ explore the full conformational space of a protein at the
+ single-molecule level, detecting even poorly populated conformers
+ and measuring their distribution in a variety of biologically
+ important conditions. To the best of our knowledge, we present
+ for the first time evidence of a conformational equilibrium that
+ controls the population of a specific class of monomeric
+ $\alpha$Syn conformers, positively correlated with conditions
+ known to promote the formation of aggregates. A new tool is thus
+ made available to test directly the influence of mutations and
+ pharmacological strategies on the conformational equilibrium of
+ monomeric $\alpha$Syn.},
+}
+
@article{ sandal09,
author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "#
AGomezCasado #" and "# BSamori,
- title = "Hooke: an open software platform for force spectroscopy.",
+ title = "Hooke: An open software platform for force spectroscopy.",
journal = BIOINFO,
year = 2009,
month = jun,
author = TKempe #" and "# SBHKent #" and "# FChow #" and "# SMPeterson
#" and "# WSundquist #" and "# JLItalien #" and "# DHarbrecht
#" and "# DPlunkett #" and "# WDeLorbe,
- title = "Multiple-copy genes: production and modification of
+ title = "Multiple-copy genes: Production and modification of
monomeric peptides from large multimeric fusion proteins.",
journal = GENE,
year = 1985,
pages = {805--809},
issn = {0364-3190},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9232632},
+ doi = {10.1023/A:1022079709085},
language = {eng},
keywords = {Alzheimer Disease},
keywords = {Amyloid beta-Peptides},
1-40, A beta 1-42 fibrils are also defibrillized in the presence
of millimolar concentrations of Ca2+. These studies suggest that
metal cations can defibrillize the fibrils of synthetic A beta.},
+ note = {From page 806, ``The exact mechanism by which these metal
+ ions affect the fibrillization of A$\beta$ is not known.''},
}
@article{ friedman05,
developed that depend upon direct ion-macromolecule interactions
as well as interactions with water molecules in the first
hydration shell of the macromolecule.},
+ note = {A quick pass through Hofmeister history, but no discussion
+ of cations (``A complete picture will inevitably involve an
+ integrated understanding of the role of cations (including
+ guanidinium ions) and osmolytes (such as urea and tri-methylamine
+ N-oxide) as well. There has been some progress in these fields,
+ although such subjects are generally beyond the scope of this
+ short review.'').},
}
@article{ isaacs06,
impaired intraneuronal calcium regulation in the aging brain and
Alzheimer disease, may play an important role in the onset of
amyloid-related pathology.},
+ note = {Physiological levels of \NaCl\ are $\sim 150\U{mM}$. \Ca\
+ is $\sim 2\U{mM}$.},
}
-@article{ itkin2011,
+@article{ itkin11,
author = AItkin #" and "# VDupres #" and "# YFDufrene #" and "#
BBechinger #" and "# JMRuysschaert #" and "# VRaussens,
title = {Calcium ions promote formation of amyloid $\beta$-peptide
fibrils. Overall, these results led us to conclude that calcium
ions stimulate the formation of oligomers of A$\beta$(1-40), that
have been implicated in the pathogenesis of AD.},
+ note = {$2\U{mM}$ of \Ca\ is the \emph{extracellular} concentration.
+ Cytosol concetrations are in the $\mu$M range.},
}
@article{ zidar11,
N-terminal parts of the fibril, whereas aggregation at higher
ionic strength is suggested to be driven by the hydrophobic
interaction.},
+ note = {Only study \NaCl\ over the range to $308\U{mM}$, but show a
+ general decreased hydrogen bonding as concentration increases.},
}
@article{ miao11,
with high affinity and specificity at biologically-relevant
concentrations. Interestingly, the binding is found to be both
salt- and residue-specific.},
+ note = {They suggest that for low concentrations ($<100\U{mM}$),
+ protein-ion interactions are mostly electrostatic. The Hofmeister
+ effects only kick in at higher consentrations.},
}
@article{ dyson05,
linkers that have a role in the assembly of macromolecular
arrays.},
}
+
+@article{ cleland64,
+ author = WWCleland,
+ title = {Dithiothreitol, a New Protective Reagent for SH Groups},
+ journal = Biochem,
+ year = 1964,
+ month = apr,
+ volume = 3,
+ number = 4,
+ pages = {480--482},
+ keywords = {Alcohols},
+ keywords = {Chromatography},
+ keywords = {Coenzyme A},
+ keywords = {Oxidation-Reduction},
+ keywords = {Research},
+ keywords = {Sulfhydryl Compounds},
+ keywords = {Sulfides},
+ keywords = {Ultraviolet Rays},
+ issn = {0006-2960},
+ doi = {10.1021/bi00892a002},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/14192894},
+ eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi00892a002},
+ language = {eng},
+}
projects / thesis.git / blobdiff